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At least 1,711 records · Page 95

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DOE OSTI2022

On the Rapid Calculation of Binding Affinities for Antigen and Antibody Design and Affinity Maturation Simulations

The accurate and efficient calculation of protein-protein binding affinities is an essential component in antibody and antigen design and optimization, and in computer modeling of antibody affinity maturation. Such calculations remain challenging despite advances in computer hardware and algorithms, primarily because proteins are flexible molecules, and thus, require explicit or implicit incorporation of multiple conformational states into the computational procedure. The astronomical size of the amino acid sequence space further compounds the challenge by requiring predictions to be computed within a short time so that many sequence variants can be tested. In this study, we compare three classes of methods for antibody/antigen (Ab/Ag) binding affinity calculations: (i) a method that relies on the physical separation of the Ab/Ag complex in equilibrium molecular dynamics (MD) simulations, (ii) a collection of 18 scoring functions that act on an ensemble of structures created using homology modeling software, and (iii) methods based on the molecular mechanics-generalized Born surface area (MM-GBSA) energy decomposition, in which the individual contributions of the energy terms are scaled to optimize agreement with the experiment. When applied to a set of 49 antibody mutations in two Ab/HIV gp120 complexes, all of the methods are found to have modest accuracy, with the highest Pearson correlations reaching about 0.6. In particular, the most computationally intensive method, i.e., MD simulation, did not outperform several scoring functions. The optimized energy decomposition methods provided marginally higher accuracy, but at the expense of requiring experimental data for parametrization. Within each method class, we examined the effect of the number of independent computational replicates, i.e., modeled structures or reinitialized MD simulations, on the prediction accuracy. We suggest using about ten modeled structures for scoring methods, and about five simulation replicates for MD simulations as a rule of thumb for obtaining reasonable convergence. We anticipate that our study will be a useful resource for practitioners working to incorporate binding affinity calculations within their protein design and optimization process.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Melter Modeling over a Range of Scales to Support Vitrification at the WTP - 19664

Computational modeling is a powerful complement to laboratory experiments and testing of systems at various scales. When properly applied and validated, computational fluid dynamics (CFD) can provide information not readily obtainable by physical testing, especially in cases where the operating environment does not permit visual observation or the insertion of typical data acquisition instrumentation as in the case of waste glass vitrification. A series of CFD and heat transfer models over a range of scales are being developed to support melter operations at the Hanford Waste Treatment and Immobilization Plant. This paper provides a description of the models and the resulting information they provide that can be used to improve melter throughput, as well as aid in evaluating and resolving operating plant issues or upsets. This work is important for the WTP operation by providing a potential for model-predictive control of the melter operation. Increases in the rate of glass production and avoiding idling can significantly decrease the duration and cost of the vitrification campaign, potentially saving billions of dollars. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

NASA NTRS1989

Development and verification of local/global analysis techniques for laminated composites

Analysis and design methods for laminated composite materials have been the subject of considerable research over the past 20 years, and are currently well developed. In performing the detailed three-dimensional analyses which are often required in proximity to discontinuities, however, analysts often encounter difficulties due to large models. Even with the current availability of powerful computers, models which are too large to run, either from a resource or time standpoint, are often required. There are several approaches which can permit such analyses, including substructuring, use of superelements or transition elements, and the global/local approach. This effort is based on the so-called zoom technique to global/local analysis, where a global analysis is run, with the results of that analysis applied to a smaller region as boundary conditions, in as many iterations as is required to attain an analysis of the desired region. Before beginning the global/local analyses, it was necessary to evaluate the accuracy of the three-dimensional elements currently implemented in the Computational Structural Mechanics (CSM) Testbed. It was also desired to install, using the Experimental Element Capability, a number of displacement formulation elements which have well known behavior when used for analysis of laminated composites.

Griffin, O. Hayden, Jr.↗

DOE OSTI2016

Meso-scale framework for modeling granular material using computed tomography

Numerical modeling of unconsolidated granular materials is comprised of multiple nonlinear phenomena. Accurately capturing these phenomena, including grain deformation and intergranular forces depends on resolving contact regions several orders of magnitude smaller than the grain size. Here, we investigate a method for capturing the morphology of the individual particles using computed X-ray and neutron tomography, which allows for accurate characterization of the interaction between grains. The ability of these numerical approaches to determine stress concentrations at grain contacts is important in order to capture catastrophic splitting of individual grains, which has been shown to play a key role in the plastic behavior of the granular material on the continuum level. Discretization approaches, including mesh refinement and finite element type selection are presented to capture high stress concentrations at contact points between grains. The effect of a grain’s coordination number on the stress concentrations is also investigated.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Comparing emulation methods for a high‐resolution storm surge model

Abstract Realistic simulations of complex systems are fundamental for climate and environmental studies. Large computer systems are often not sufficient to run sophisticated computational models for large numbers of different input settings. Statistical surrogate models, or emulators, are key tools enabling fast exploration of the simulator input space. Gaussian processes have become standard for computer simulator emulation. However, they require careful implementation to scale appropriately, motivating alternative methods more recently introduced. We present a comparison study of surrogates of the Sea, Lake, and Overland Surges from Hurricanes (SLOSH) simulator—the simulator of choice for government agencies—using four emulation approaches: BASS; BART; SEPIA; and RobustGaSP. SEPIA and RobustGaSP use Gaussian processes, BASS implements adaptive splines, and BART is based on ensembles of regression trees. We describe the four models and compare them in terms of computation time and predictive metrics. These surrogates use proven and distinct methodologies, are available through accessible software, and quantify prediction uncertainty. Our data cover millions of response values. We find that SEPIA and RobustGaSP provide exceptional predictive power, but cannot scale to emulate experiments as large as the one considered in this paper as effectively as BASS and BART.

Hutchings, Grant↗

NASA NTRS1993

Mathematical description of complex chemical kinetics and application to CFD modeling codes

A major effort in combustion research at the present time is devoted to the theoretical modeling of practical combustion systems. These include turbojet and ramjet air-breathing engines as well as ground-based gas-turbine power generating systems. The ability to use computational modeling extensively in designing these products not only saves time and money, but also helps designers meet the quite rigorous environmental standards that have been imposed on all combustion devices. The goal is to combine the very complex solution of the Navier-Stokes flow equations with realistic turbulence and heat-release models into a single computer code. Such a computational fluid-dynamic (CFD) code simulates the coupling of fluid mechanics with the chemistry of combustion to describe the practical devices. This paper will focus on the task of developing a simplified chemical model which can predict realistic heat-release rates as well as species composition profiles, and is also computationally rapid. We first discuss the mathematical techniques used to describe a complex, multistep fuel oxidation chemical reaction and develop a detailed mechanism for the process. We then show how this mechanism may be reduced and simplified to give an approximate model which adequately predicts heat release rates and a limited number of species composition profiles, but is computationally much faster than the original one. Only such a model can be incorporated into a CFD code without adding significantly to long computation times. Finally, we present some of the recent advances in the development of these simplified chemical mechanisms.

Bittker, D. A.↗

NASA NTRS1993

Mathematical Description of Complex Chemical Kinetics and Application to CFD Modeling Codes

Bittker, D. A.↗

DOE OSTI2019

Nonequilibrium Phenomena in (Quasi-)thermal Plasma Flows

Thermal plasmas are utilized in diverse applications that require high power densities or throughputs, such as metal cutting, welding, spraying, metallurgy, and materials synthesis. Thermal plasma applications involve interactions between the highly energetic plasma and working gas streams, confining devices, or processing materials. Whereas thermal plasma implies a state of equilibrium (i.e. Local Thermodynamic Equilibrium, LTE), due to the above interactions, thermal plasma flows depict nonequilibrium phenomena of two types: kinetic and dissipative. Kinetic nonequilibrium manifests microscopically and is caused by localized imbalances between particles and fields interactions. Its occurrence is illustrated, for example, as deviations from thermal equilibrium between heavy-species and electrons or from mass-action laws. In contrast, dissipative nonequilibrium reveals macroscopically and is produced by external driving forces that incite distributed responses, such as the growth of instabilities, the occurrence of self-organization, or the establishment of turbulence. While kinetic nonequilibrium has been increasingly incorporated in thermal plasma flow models (e.g. finite-rate chemistry, two-temperature models), it is the great advances in numerical computing that is enabling the exploration of dissipative nonequilibrium (e.g. pattern formation, small-scale turbulent features). Both types of nonequilibrium are reviewed, including their estimation and incidence, within the context of computational models and their relevance to thermal plasma sources and processes.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2025

Unpacking model inadequacy: The quantification of silver release from TRISO fuel by considering empirical and mechanistic approaches

Increasing adoption of the proposed tristructural isotropic (TRISO) particle fuel for both advanced and existing reactors makes it critical to assess and address any uncertainties and inadequacies of TRISO fission product release models. Model inadequacy stems from simplifications made to the computational model when compared to the experiments. The modeling and simulation efforts conducted using the BISON fuel performance code, along with the experimental campaigns carried out under the Advanced Gas Reactor Fuel Development and Qualification Program, afford a unique opportunity to conduct a rigorous modeling inadequacy assessment within the Bayesian uncertainty quantification (UQ) framework. Here, this study compares the standard Bayesian framework against the Kennedy-O'Hagan (KOH) framework, which explicitly represents modeling inadequacy, in regard to UQ for TRISO silver release models. For this purpose, both the traditional Arrhenius equation fitted to experimental data and the more advanced lower-length-scale (LLS)-informed model, which considers microstructure information, are independently considered. Applying the inverse UQ process on the AGR-2 and -3/4 datasets revealed modeling inadequacy to be the most dominant source of uncertainty. Experimental noise uncertainty is also significant; however, model parameter uncertainty can be considered negligible. Interestingly, both the Arrhenius equation and the LLS-informed model demonstrated similar levels of modeling inadequacy. For the forward predictive UQ, the KOH framework improved both the accuracy and quality of quantified uncertainties in comparison to the standard Bayesian framework. This is true for both the Arrhenius equation and the LLS-informed model. In comparing these modeling approaches, both demonstrated similar performance at the engineering scale, while the LLS-informed model expectedly outperformed the Arrhenius equation at the mesoscale. These conclusions highlight the importance of explicitly accounting for modeling inadequacy in the UQ process, and reinforce the need for continuous refinement of physics-based models in order to address the modeling inadequacy.

Advanced reactors↗

DOE OSTI2023

Domain crossover in the reductase subunit of NADPH-dependent assimilatory sulfite reductase

NADPH-dependent assimilatory sulfite reductase (SiR) from Escherichia coli performs a six-electron reduction of sulfite to the bioavailable sulfide. SiR is composed of a flavoprotein (SiRFP) reductase subunit and a hemoprotein (SiRHP) oxidase subunit. There is no known high-resolution structure of SiR or SiRFP, thus we do not yet fully understand how the subunits interact to perform their chemistry. Here, we used small-angle neutron scattering to understand the impact of conformationally restricting the highly mobile SiRFP octamer into an electron accepting (closed) or electron donating (open) conformation, showing that SiR remains active, flexible, and asymmetric even with these conformational restrictions. From these scattering data, we then model the first solution structure of SiRFP. Further, computational modeling of the N-terminal 52 amino acids that are responsible for SiRFP oligomerization suggests an eight-helical bundle tethers together the SiRFP subunits to form the SiR core. Finally, mass spectrometry analysis of the closed SiRFP variant show that SiRFP is capable of inter-molecular domain crossover, in which the electron donating domain from one polypeptide is able to interact directly with the electron accepting domain of another polypeptide. This structural characterization suggests that SiR performs its high-volume electron transfer through both inter- and intramolecular pathways between SiRFP domains and, thus, cis or trans transfer from reductase to oxidase subunits. Such highly redundant potential for electron transfer makes this system a potential target for designing synthetic enzymes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Pareto Optimality Explanation of the Glycolytic Alternatives in Nature

The Entner-Doudoroff (ED) and Embden-Meyerhof-Parnas (EMP) glycolytic pathways are largely conserved across glycolytic species in nature. Is this a coincidence, convergent evolution or there exists a driving force towards either of the two pathway designs? We addressed this question by first employing a variant of the optStoic algorithm to exhaustively identify over 11,916 possible routes between glucose and pyruvate at different pre-determined stoichiometric yields of ATP. Subsequently, we analyzed the thermodynamic feasibility of all the pathways at physiological metabolite concentrations and quantified the protein cost of the feasible solutions. Pareto optimality analysis between energy efficiency and protein cost reveals that the naturally evolved ED and EMP pathways are indeed among the most protein cost-efficient pathways in their respective ATP yield categories and remain thermodynamically feasible across a wide range of ATP/ADP ratios and pathway intermediate metabolite concentration ranges. In contrast, pathways with higher ATP yield (>2) while feasible, are bound within stringent and often extreme operability ranges of cofactor and intermediate metabolite concentrations. The preponderance of EMP and ED is thus consistent with not only optimally balancing energy yield vs. enzyme cost but also with ensuring operability for wide metabolite concentration ranges and ATP/ADP ratios.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Rapid data acquisition and machine learning-assisted composition design of functionally graded alloys via wire arc additive manufacturing

Abstract The lack of high-quality datasets in materials science hinders artificial intelligence (AI)-driven alloy design. To address this challenge, wire arc additive manufacturing (WAAM) was employed to fabricate graded alloys, generating extensive data for machine learning (ML)-assisted property prediction. ML models were developed using high-throughput experiments, computational models, and genetic algorithm to optimize feature selection, successfully predicting hardness and porosity. The ML model demonstrated its efficacy by designing a gradient alloy with enhanced properties. However, scaling up revealed uncertainties in tensile property and porosity due to differences in size and thermal conditions between the designed alloy build and the gradient print used to construct the ML model. This underscores the need for uncertainty quantification and process optimization in WAAM-driven alloy design. Our work advances AI-integrated additive manufacturing, offering a rapid approach to exploring process–structure–property relationships and accelerating materials development.

Wang, Xin↗

NASA NTRS1977

Prediction of pilot reserve attention capacity during air-to-air target tracking

Reserve attention capacity of a pilot was calculated using a pilot model that allocates exclusive model attention according to the ranking of task urgency functions whose variables are tracking error and error rate. The modeled task consisted of tracking a maneuvering target aircraft both vertically and horizontally, and when possible, performing a diverting side task which was simulated by the precise positioning of an electrical stylus and modeled as a task of constant urgency in the attention allocation algorithm. The urgency of the single loop vertical task is simply the magnitude of the vertical tracking error, while the multiloop horizontal task requires a nonlinear urgency measure of error and error rate terms. Comparison of model results with flight simulation data verified the computed model statistics of tracking error of both axes, lateral and longitudinal stick amplitude and rate, and side task episodes. Full data for the simulation tracking statistics as well as the explicit equations and structure of the urgency function multiaxis pilot model are presented.

Onstott, E. D.↗

NASA NTRS1980

Handling qualities of large flexible control-configured aircraft

The effects on handling qualities of low frequency symmetric elastic mode interaction with the rigid body dynamics of a large flexible aircraft was analyzed by use of a mathematical pilot modeling computer simulation. An extension of the optimal control model for a human pilot was made so that the mode interaction effects on the pilot's control task could be assessed. Pilot ratings were determined for a longitudinal tracking task with parametric variations in the undamped natural frequencies of the two lowest frequency symmetric elastic modes made to induce varying amounts of mode interaction. Relating numerical performance index values associated with the frequency variations used in several dynamic cases, to a numerical Cooper-Harper pilot rating has proved successful in discriminating when the mathematical pilot can or cannot separate rigid from elastic response in the tracking task.

Swaim, R. L.↗

NASA NTRS1984

Some mathematical tools for a modeller's workbench

The development of a mathematical software tools in workbench environment to model related objects more straightforward is outlined. A computer model from informal drawings and a plastic model of a helicopter is discussed. Lofting was the predominant, characteristic modelling technique. Ships and airplane designs use lofting as a technique because they have defined surfaces, (hulls and fuselages) from vertical station cuts perpendicular to the vertical center plane defining the major axis of reflective symmetry. A turbine blade from a jet engine was modelled in this way. The aerodynamic portion and the root comes from different paradigms. The union of these two parts into a coherent model is shown.

Cohen, E.↗

NASA NTRS1987

Temperatures and minimum thickness of the inactive surface layer of comet Halley

The effects of a nonvolatile mantle on the thermal state of a comet nucleus are investigated. The original computer model was modified so that temperatures can be computed through a thin dust mantle to the center of a 5 km spherical nucleus in the orbit of P/Halley. No attempt is made to simulate the formation of the mantle. Results are obtained for various specified values of initial mantle thickness and thermal conductivity to determine their effects on temperature profiles through the mantle. The minimum thickness of mantle that can withstand ejection by sublimating gasses is also calculated as a function of mantle thermal conductivity. Calculations were performed for ten or more orbits until temperatures in the mantle reached a near steady state. Results indicate that mantles as thin as 4 cm and 14 cm, for thermal conductivities of 600 and 6000 ergs/cm/s K, respectively, will remain intact. Surface temperatures as high as 511 K at perihelion and 400 K at the position of spacecraft encounter were computed at 0 degree latitude for an upright, rotating nucleus. Ice interface temperatures were raised by different amounts during each orbit, depending on mantle thickness and thermal conductivity, until steady state was reached. These results imply that relatively small nonvolatile masses emplaced randomly in comet nuclei could produce an irregular, permanently mantled surface and could also account for the apparently random location of active areas.

Fanale, F. P.↗

NASA NTRS1990

Capillary Pumped Loop Modeler

Capillary Pumped Loop (CPL) Modeler computer program is amalgamation of software that mathematically models performance of CPL system and its environment. Two-phase heat-transport device capable of transferring heat loads efficiently over large distance with little temperature differential. Utilizes surface-tension forces established in fine-pore capillary wick to circulate working fluid, requiring no external pumpling power. Predicts steady-state or quasi-steady behavior of CPL embedded in spacecraft or other thermal environment. Also predicts location of liquid/vapor interface in each condenser. Written in VAX/VMS FORTAN 77.

Ku, Jentung↗

NASA NTRS1994

Technology transfer of operator-in-the-loop simulation

The technology developed for operator-in-the-loop simulation in space teleoperation has been applied to Caterpillar's backhoe, wheel loader, and off-highway truck. On an SGI workstation, the simulation integrates computer modeling of kinematics and dynamics, real-time computational and visualization, and an interface with the operator through the operator's console. The console is interfaced with the workstation through an IBM-PC in which the operator's commands were digitized and sent through an RS-232 serial port. The simulation gave visual feedback adequate for the operator in the loop, with the camera's field of vision projected on a large screen in multiple view windows. The view control can emulate either stationary or moving cameras. This simulator created an innovative engineering design environment by integrating computer software and hardware with the human operator's interactions. The backhoe simulation has been adopted by Caterpillar in building a virtual reality tool for backhoe design.

Yae, K. H.↗